Fig. 2

Higher resolution characterization of CSF cells in treatment-naïve MS vs control patients. A UMAP plot of level 2 clustering in merged control (Ctrl) and MS with automatic annotation based on canonical marker genes [18] (Additional file 8: Tab. S4). Cluster key (as not listed Fig. 1): ASDC, AXL⁺ SIGLEC6⁺ dendritic cells; CD4 CTL, CD4⁺ cytotoxic T lymphocyte; CD4/CD8 TCM, CD4⁺/CD8⁺ memory T cell; CD4/CD8 TEM, CD4⁺/CD8⁺ T effector memory cell; Eryth, erythrocytes; HSPC, hematopoietic stem and progenitor cell; ILC, innate lymphoid cell; MAIT, mucosal associated invariant T cell; NK, natural killer cell; Treg, regulatory T cell; cDC1/DC2, conventional dendritic cell; dnT, double-negative T cell; gdT, gamma delta T cell; pDC, plasmacytoid dendritic cell. B Volcano plot visualizing cluster abundance in Ctrl compared to MS of level 2 clustering plotted as fold change (log2) against t-test p value (-log10). Please note that the number of cells in some Ctrl clusters (e.g., Bc naïve) was insufficient to calculate the fold change. Clusters highlighted in blue are upregulated in MS and represent clusters of interest. C Left stacked bar plot showing the relative distribution of B cell subclusters in Ctrl compared to MS. Each cluster is set to 100% irrespective of its abundance. Right stacked bar plot showing the total number of B cell clusters in Ctrl vs MS. D Heatmap visualizing expression of immunoglobulin and other selected genes in B cell clusters. Expression values were normalized per gene with 0 reflecting the lowest and 10 reflecting the highest expression, visualized via color intensity. E Dot plot of selected signature genes for gdT cells in MS compared to Ctrl. Dot size represents the fraction of cells expressing the gene, color intensity shows the mean expression. F Precomputed differential expressed genes by cellxgene VIP of selected marker genes of gdT cells. Color coding shows significant up- (red) or downregulation (blue) in MS compared to Ctrl, dot size encodes the fold change. FDR > 0.1